join_units_2 {rhierbaps}

join_units_2

Description

Peform an iteration of the second move in the algorithm. That is combine two clusters to improve the marginal likelihood.

Usage

join_units_2(
  snp.object,
  partition,
  threshold = 1e-05,
  n.cores = 1,
  comb.chache = NULL
)

Arguments

snp.object

A snp.object containing the processed SNP data.

partition

An integer vector indicating an initial partition of the isolates.

threshold

The increase in marginal log likelihood required to accept a move.

n.cores

The number of cores to use.

comb.chache

a matrix recording previous marginal llks of combining clusters

Value

The best partition after combining two clusters as well as a boolean value indicating whether a move increased the marginal likelihood.